Remove jetty workaround.

src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSinkUnitTest.java

@@ -39,11 +39,6 @@ public class ReadsSparkSinkUnitTest extends GATKBaseTest {
 
     @BeforeClass(alwaysRun = true)
     private void setupMiniCluster() throws IOException {
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         cluster = MiniClusterUtils.getMiniCluster();
     }
 

src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSourceUnitTest.java

@@ -196,10 +196,6 @@ public void testReadFromFileAndHDFS() throws Exception {
         final GATKPath bam = new GATKPath(getTestFile("hdfs_file_test.bam").getAbsolutePath());
         final File bai = getTestFile("hdfs_file_test.bai");
         // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);
             final Path bamPath = new Path(workingDirectory,"hdfs.bam");
@@ -223,11 +219,6 @@ public void testCRAMReferenceFromHDFS() throws Exception {
         final GATKPath reference = new GATKPath(v37_chr17_1Mb_Reference);
         final GATKPath referenceIndex = new GATKPath(v37_chr17_1Mb_Reference + ".fai");
 
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);
             final Path cramHDFSPath = new Path(workingDirectory, "hdfs.cram");

src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java

@@ -52,11 +52,6 @@ public final class VariantsSparkSinkUnitTest extends GATKBaseTest {
 
     @BeforeClass(alwaysRun = true)
     private void setupMiniCluster() throws IOException {
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         cluster = MiniClusterUtils.getMiniCluster();
     }
 

src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java

@@ -116,11 +116,6 @@ public void testInsertLengthPileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testFeaturesPileupHdfs(boolean useShuffle) throws Exception {
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);
             final Path vcfPath = new Path(workingDirectory, "dbsnp_138.b37.20.21.vcf");

src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java

@@ -80,11 +80,6 @@ public void testReadAndWriteCRAMAndReferenceOnHDFS() throws Exception {
         final GATKPath testRefDict = new GATKPath(getTestFile("count_reads.dict").getAbsolutePath());
         final GATKPath testRefIndex = new GATKPath(getTestFile("count_reads.fasta.fai").getAbsolutePath());
 
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> {
             final org.apache.hadoop.fs.Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);
 

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/CpxVariantReInterpreterSparkIntegrationTest.java

@@ -71,11 +71,6 @@ public void testRunLocal(final CpxVariantReInterpreterSparkIntegrationTestArgs p
 
     @Test(groups = "sv", dataProvider = "forCpxVariantReInterpreterSparkIntegrationTest")
     public void testRunHDFS(final CpxVariantReInterpreterSparkIntegrationTestArgs params) throws Exception {
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> {
 
             final List<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest.java

@@ -68,11 +68,6 @@ public void testDiscoverVariantsRunnableLocal(final DiscoverVariantsFromContigAl
     @Test(dataProvider = "discoverVariantsFromContigAlignmentsSparkIntegrationTest", groups = "sv")
     public void testDiscoverVariantsRunnableMiniCluster(final DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTestArgs params) throws Exception {
 
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> {
 
             final List<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/FindBreakpointEvidenceSparkIntegrationTest.java

@@ -115,11 +115,6 @@ public void testFindBreakpointRunnableLocal(final FindBreakpointEvidenceSparkInt
     @Test(dataProvider = "findBreakpointEvidenceSparkIntegrationTest", groups = "sv")
     public void testFindBreakpointRunnableMiniCluster(final FindBreakpointEvidenceSparkIntegrationTestArgs params) throws Exception {
 
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> {
 
             final List<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

src/test/java/org/broadinstitute/hellbender/tools/spark/sv/integration/StructuralVariationDiscoveryPipelineSparkIntegrationTest.java

@@ -116,11 +116,6 @@ public void testSVDiscoverPipelineRunnableLocal(final StructuralVariationDiscove
     @Test(dataProvider = "svDiscoverPipelineSparkIntegrationTest", groups = "sv")
     public void testSVDiscoverPipelineRunnableMiniCluster(final StructuralVariationDiscoveryPipelineSparkIntegrationTestArgs params) throws Exception {
 
-        if (isGATKDockerContainer()) {
-            // see https://github.com/eclipse/jetty.project/issues/8549
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster(cluster -> {
 
             final List<String> argsToBeModified = Arrays.asList( new ArgumentsBuilder().addRaw(params.getCommandLine()).getArgsArray() );

src/test/java/org/broadinstitute/hellbender/utils/gcs/BucketUtilsUnitTest.java

@@ -202,11 +202,6 @@ public void testCopyAndDeleteHDFS() throws Exception {
         final String src = publicTestDir + "empty.vcf";
         File dest = createTempFile("copy-empty", ".vcf");
 
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             final String intermediate = BucketUtils.randomRemotePath(MiniClusterUtils.getWorkingDir(cluster).toString(), "test-copy-empty", ".vcf");
             Assert.assertTrue(BucketUtils.isHadoopUrl(intermediate), "!BucketUtils.isHadoopUrl(intermediate)");

src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java

@@ -465,11 +465,6 @@ public void testAppendPathToDir() throws Exception {
         Assert.assertEquals(IOUtils.appendPathToDir("dir/", "/file"), "/file");
         Assert.assertEquals(IOUtils.appendPathToDir("/path/to/dir", "anotherdir/file"), "/path/to/dir/anotherdir/file");
 
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         // hdfs: URI
         MiniDFSCluster cluster = null;
         try {
@@ -534,11 +529,6 @@ public void testUnsuccessfulCanReadFileCheck(final File file) {
     @Test
     public void testCreateDirectory() throws IOException {
 
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         // hdfs
         Path tempPath = IOUtils.getPath(MiniClusterUtils.getWorkingDir(MiniClusterUtils.getMiniCluster()).toUri().toString())
                 .resolve("temp");

src/test/java/org/broadinstitute/hellbender/utils/spark/SparkUtilsUnitTest.java

@@ -74,11 +74,6 @@ public void testConvertHeaderlessHadoopBamShardToBam() {
 
     @Test
     public void testPathExists() throws Exception {
-        // see https://github.com/eclipse/jetty.project/issues/8549
-        if (isGATKDockerContainer()) {
-            // for the docker tests, the test dependencies are in a separate jar
-            throw new SkipException("skipping due to jetty jar parsing issues (https://github.com/eclipse/jetty.project/issues/8549)");
-        }
         MiniClusterUtils.runOnIsolatedMiniCluster( cluster -> {
             //use the HDFS on the mini cluster
             final Path workingDirectory = MiniClusterUtils.getWorkingDir(cluster);